Variant report

Variant	rs225624
Chromosome Location	chr6:142471340-142471341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142467284..142470196-chr6:142471245..142474194,3	MCF-7	breast:
2	chr6:142470533..142472236-chr6:142476885..142478577,2	K562	blood:
3	chr6:142470687..142472679-chr6:142481549..142483699,2	K562	blood:
4	chr6:142470468..142472219-chr6:144162798..144164527,2	K562	blood:
5	chr6:142469818..142472806-chr6:142621459..142623184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009844	Chromatin interaction
ENSG00000135521	Chromatin interaction
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11758623	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs178783	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs225601	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225602	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs225605	0.93[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap]
rs225606	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225618	0.93[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs225622	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225628	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225630	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225631	0.93[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225632	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225633	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225634	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225635	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225636	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225639	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225640	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225641	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225642	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225643	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225648	0.83[TSI][hapmap]
rs225650	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225651	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225652	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225653	0.84[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225654	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225655	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225656	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225657	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225658	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225659	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225660	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225661	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs225662	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225663	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225664	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225665	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225666	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225667	0.81[ASN][1000 genomes]
rs225668	0.81[ASN][1000 genomes]
rs225670	0.81[ASN][1000 genomes]
rs225671	0.81[ASW][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225672	0.81[ASN][1000 genomes]
rs225673	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225674	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225675	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225676	0.81[ASW][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs225677	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225678	1.00[JPT][hapmap]
rs225679	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225684	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs225685	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225687	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs225689	1.00[JPT][hapmap]
rs225695	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225700	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225701	1.00[JPT][hapmap]
rs225702	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225710	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs4896574	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4896575	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs56185739	0.81[ASN][1000 genomes]
rs62430473	0.82[ASN][1000 genomes]
rs628311	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639658	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6939944	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939975	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.81[JPT][hapmap]
rs9389979	0.81[JPT][hapmap]
rs9389980	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225624	VTA1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142468800-142472200	Weak transcription	Pancreas	Pancrea
2	chr6:142468800-142488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:142469200-142471600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:142469200-142477000	Weak transcription	Stomach Mucosa	stomach
5	chr6:142469200-142483400	Weak transcription	Aorta	Aorta
6	chr6:142469200-142487800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:142469400-142471600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr6:142469600-142471600	Weak transcription	Left Ventricle	heart
9	chr6:142469600-142472200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:142469600-142487800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:142469600-142487800	Weak transcription	Thymus	Thymus
12	chr6:142469800-142472600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:142469800-142481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:142469800-142487600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:142470000-142471400	Weak transcription	Fetal Thymus	thymus
16	chr6:142470000-142472000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:142470000-142476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:142470000-142477000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:142470000-142477200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:142470000-142481400	Weak transcription	Gastric	stomach
21	chr6:142470000-142484000	Weak transcription	Psoas Muscle	Psoas
22	chr6:142470000-142486400	Weak transcription	Fetal Intestine Small	intestine
23	chr6:142470200-142472000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:142470200-142474000	Weak transcription	NH-A	brain
25	chr6:142470200-142484000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:142470200-142487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
30	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
31	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
32	chr6:142470400-142471400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:142470400-142471400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:142470400-142471600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:142470400-142471600	Active TSS	Brain Germinal Matrix	brain
36	chr6:142470400-142471800	Enhancers	Liver	Liver
37	chr6:142470400-142472000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr6:142470400-142472000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:142470400-142472200	Weak transcription	Ovary	ovary
40	chr6:142470400-142473400	Weak transcription	Osteobl	bone
41	chr6:142470400-142473800	Weak transcription	A549	lung
42	chr6:142470400-142473800	Weak transcription	Hela-S3	cervix
43	chr6:142470400-142473800	Weak transcription	NHEK	skin
44	chr6:142470400-142473800	Weak transcription	NHLF	lung
45	chr6:142470400-142474000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:142470400-142476200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:142470400-142476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:142470400-142476800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:142470400-142476800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:142470400-142477000	Weak transcription	Adipose Nuclei	Adipose

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